Simultaneous profiling of seed-associated bacteria and fungi reveals antagonistic interactions between microorganisms within a shared epiphytic microbiome on Triticum and Brassica seeds.

Matthew G Links,Tom Gräfenhan,Janet E Hill,Tigst Demeke,Tim J Dumonceaux,Sean M Hemmingsen

doi:10.1111/nph.12693

Abstract

In order to address the hypothesis that seeds from ecologically and geographically diverse plants harbor characteristic epiphytic microbiota, we characterized the bacterial and fungal microbiota associated with Triticum and Brassica seed surfaces.The total microbial complement was determined by amplification and sequencing of a fragment of chaperonin 60 (cpn60). Specific microorganisms were quantified by qPCR. Bacteria and fungi corresponding to operational taxonomic units (OTU) that were identified in the sequencing study were isolated and their interactions examined.A total of 5477 OTU were observed from seed washes. Neither total epiphytic bacterial load nor community richness/evenness was significantly different between the seed types; 578 OTU were shared among all samples at a variety of abundances. Hierarchical clustering revealed that 203 were significantly different in abundance on Triticum seeds compared with Brassica. Microorganisms isolated from seeds showed 99–100% identity between the cpn60 sequences of the isolates and the OTU sequences from this shared microbiome. Bacterial strains identified as Pantoea agglomerans had antagonistic properties toward one of the fungal isolates (Alternaria sp.), providing a possible explanation for their reciprocal abundances on both Triticum and Brassica seeds.cpn60 enabled the simultaneous profiling of bacterial and fungal microbiota and revealed a core seed-associated microbiota shared between diverse plant genera.

Highlights

The seeds of crops such as wheat (Triticum spp.) and canola (Brassica spp.) are products of agricultural enterprise and the source of the generation of plants
By comparing the assembled operational taxonomic units (OTU) sequences with those from bacteria and fungi isolated from these samples we demonstrated that OTU could be assembled de novo with 100% identity to microbes in complex samples
The total 16S rRNA gene copy number associated with each Triticum seed type varied over a range of c. 4-fold, with Wheat-4 (CWRS grade 1) being the lowest and Wheat-2 (CWAD grade 3) the highest (Fig. 1)

Summary

Introduction

The seeds of crops such as wheat (Triticum spp.) and canola (Brassica spp.) are products of agricultural enterprise and the source of the generation of plants. Like other parts of the plant, are colonized by an epiphytic microbiota consisting of synergistic, commensal and potentially pathogenic microbes that play a crucial role in health and susceptibility to disease (Hashidoko, 2005; Critzer & Doyle, 2010). Because the plant-associated microbiota clearly plays a role in plant fitness (Hallmann et al, 1997), different crops might be expected to harbor distinct microbiota on their seed surfaces and the constituents of these microbial communities are likely to have functional relevance during plant growth, development and seed storage. The potential impact of crop-based microbial communities on yields and on pest control demands that a comprehensive knowledge of microbiota associated with seed surfaces be elucidated

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Conclusion